This is the source code for the Smith Waterman performance example.

```java /*

* Jun 25, 2008 Copyright (c) ZBiT, University of Tübingen, Germany
* Compiler: JDK 1.6.0
*/

/**

* @author Andreas Dräger (draeger) andreas.draeger@uni-tuebingen.de
* @date Jun 25, 2008
*/

public class AlignmentTest {

      /**
       * This method computes a pairwise local alignment between two given sequences
       * and prints the result on the standard output stream. The sequences must be
       * genbank files and the substitution matrix must be defined for the same
       * alphabet than both sequences.
       *
       * @param args
       *          query sequence file (genbank), subject sequence file (genbank),
       *          substitution matrix file

       */
      public static void main(String[] args) {
              try {
                      RichSequenceIterator rsiQuery = org.biojavax.bio.seq.RichSequence.IOTools
                          .readGenbankDNA(new BufferedReader(new FileReader(args[0])),
                              RichObjectFactory.getDefaultNamespace());
                      RichSequenceIterator rsiSubject = org.biojavax.bio.seq.RichSequence.IOTools
                          .readGenbankDNA(new BufferedReader(new FileReader(args[1])),
                              RichObjectFactory.getDefaultNamespace());
                      if (rsiQuery.hasNext() && rsiSubject.hasNext()) {
                              RichSequence query = rsiQuery.nextRichSequence();
                              RichSequence subject = rsiSubject.nextRichSequence();
                              SequenceAlignment sa = new SmithWaterman(0, 5, 2, 2, 1,
                                  new SubstitutionMatrix((FiniteAlphabet) query.getAlphabet(),
                                      new File(args[2])));
                              sa.pairwiseAlignment(query, subject);
                              System.out.println(sa.getAlignmentString());
                      }
              } catch (FileNotFoundException e) {
                      e.printStackTrace();
              } catch (NoSuchElementException e) {
                      e.printStackTrace();
              } catch (BioException e) {
                      e.printStackTrace();
              } catch (IOException e) {
                      e.printStackTrace();
              } catch (Exception e) {
                      e.printStackTrace();
              }
      }

} ```